Journal Article

Persistent detection of alternatively spliced BCR‐ABL variant results in a failure to achieve deep molecular response

Tanimoto, Mitsune, Miyamoto, Toshihiro, Semba, Yuichiro, Ohkawa, Yasuyuki, Yamamoto, Kazuhito, Miyamura, Koichi, Taniwaki, Masafumi, Akashi, Koichi, Hayashi, Masayasu, Yuda, Junichiro, Odawara, Jun

2017

Overview

Treatment with tyrosine kinase inhibitors (TKI) may sequentially induce TKI‐resistant BCR‐ABL mutants in chronic myeloid leukemia (CML). Conventional PCR monitoring of BCR‐ABL is an important indicator to determine therapeutic intervention for preventing disease progression. However, PCR cannot separately quantify amounts of BCR‐ABL and its mutants, including alternatively spliced BCR‐ABL with an insertion of 35 intronic nucleotides (BCR‐ABLIns35bp) between ABL exons 8 and 9, which introduces the premature termination and loss of kinase activity. To assess the clinical impact of BCR‐ABL mutants, we performed deep sequencing analysis of BCR‐ABL transcripts of 409 samples from 37 patients with suboptimal response to frontline imatinib who were switched to nilotinib. At baseline, TKI‐resistant mutations were documented in 3 patients, whereas BCR‐ABLIns35bp was detected in all patients. After switching to nilotinib, both BCR‐ABL and BCR‐ABLIns35bp became undetectable in 3 patients who attained complete molecular response (CMR), whereas in the remaining all 34 patients, BCR‐ABLIns35bp was persistently detected, and minimal residual disease (MRD) fluctuated at low but detectable levels. PCR monitoring underestimated molecular response in 5 patients whose BCR‐ABLIns35bp was persisted, although BCR‐ABLIns35bp does not definitively mark TKI resistance. Therefore, quantification of BCR‐ABLIns35bp is useful for evaluating “functional” MRD and determining the effectiveness of TKI with accuracy. Deep sequencing analysis revealed that BCR‐ABLIns35bp persisted and fluctuated at low levels in patients who failed to achieved DMR, resulting in underestimating of molecular response status to TKI therapy. Therefore, separate quantification of BCR‐ABL, “function‐dead” BCR‐ABLIns35bp and TKI‐resistant KD mutations enables us to determine the effectiveness of TKI therapy with accuracy.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Alternative splicing / Alternative Splicing - drug effects / Alternative Splicing - genetics / BCR-ABL protein / BCR‐ ABL I ns35bp / Chronic myeloid leukemia / deep sequencing / Drug Resistance, Neoplasm - drug effects / Drug Resistance, Neoplasm - genetics / Exons / Exons - drug effects / Female / Fusion Proteins, bcr-abl - genetics / High-Throughput Nucleotide Sequencing / Humans / Imatinib / Introns - drug effects / Kinases / Leukemia, Myelogenous, Chronic, BCR-ABL Positive - drug therapy / Leukemia, Myelogenous, Chronic, BCR-ABL Positive - genetics / Leukemia, Myelogenous, Chronic, BCR-ABL Positive - pathology / Male / Minimal residual disease / Mutation / Myeloid leukemia / Nucleotides / Original / Patients / Protein Kinase Inhibitors - administration & dosage / Protein-tyrosine kinase / Pyrimidines - administration & dosage / RNA polymerase / Sensors / splicing variant / Studies